Identification of CAF-related lncRNAs at the pan-cancer level represents a potential carcinogenic risk.

Cancer-associated fibroblasts (CAFs) are increasingly recognized as playing a crucial role in regulating cancer progression and metastasis. These cells can be activated by long non-coding RNAs (lncRNAs), promoting the malignant biological processes of tumor cells. Therefore, it is essential to understand the regulatory relationship between CAFs and lncRNAs in cancers. Here, we identified CAF-related lncRNAs at the pan-cancer level to systematically predict their potential regulatory functions. The identified lncRNAs were also validated using various external data at both tissue and cellular levels. This study has revealed that these CAF-related lncRNAs exhibit expression perturbations in cancers and are highly correlated with the infiltration of stromal cells, particularly fibroblasts and endothelial cells. By prioritizing a list of CAF-related lncRNAs, we can further distinguish patient subtypes that show survival and molecular differences. In addition, we have developed a web server, CAFLnc (https://46906u5t63.zicp.fun/CAFLnc/), to visualize our results. In conclusion, CAF-related lncRNAs hold great potential as a valuable resource for comprehending lncRNA functions and advancing the identification of biomarkers for cancer progression and therapeutic targets in cancer treatment.

SIRT5 promote malignant advancement of chordoma by regulating the desuccinylation of c-myc.

Chordoma is a relatively rare and locally aggressive malignant tumor. Sirtuin (SIRT)5 plays pivotal roles in various tumors, but the role of SIRT5 in chordoma has not been found. This study was performed to investigate the regulatory effects of SIRT5 on cell proliferation, migration, and invasion and the underlying mechanism in chordoma. A xenograft tumor mouse model was established to assess tumor growth. Reverse transcription-quantitative polymerase chain reaction was used to analyze the mRNA levels of SIRT5 and c-myc. The effects of SIRT5 and c-myc on cell proliferation, migration, and invasion of chordoma cells were detected by cell counting kit-8, colony formation, and Transwell assays. The interaction between SIRT5 and c-myc was evaluated by co-immunoprecipitation (IP) assay. The succinylation of c-myc was analyzed by IP and Western blot. The results showed that SIRT5 expression was upregulated in chordoma tissues and cells. SIRT5 interacted with c-myc to inhibit the succinylation of c-myc at K369 site in human embryonic kidney (HEK)-293T cells. Silencing of SIRT5 suppressed the cell proliferation, migration, and invasion of chordoma cells, while the results were reversed after c-myc overexpression. Moreover, silencing SIRT5 suppressed tumor growth in mice. These findings suggested that SIRT5 promoted the malignant advancement of chordoma by regulating the desuccinylation of c-myc.

The interaction effects of zinc and polygenic risk score with benzo[a]pyrene exposure on lung cancer risk: A prospective case-cohort study among Chinese populations.

The relationship of exposure to benzo[a]pyrene (BaP) with lung cancer risk has been firmly established, but whether this association could be modified by other environmental or genetic factors remains to be explored. To investigate whether and how zinc (Zn) and genetic predisposition modify the association between BaP and lung cancer, we performed a case-cohort study with a 5.4-year median follow-up duration, comprising a representative subcohort of 1399 participants and 359 incident lung cancer cases. The baseline concentrations of benzo[a]pyrene diol epoxide-albumin adduct (BPDE-Alb) and Zn were quantified. We also genotyped the participants and computed the polygenic risk score (PRS) for lung cancer. Our findings indicated that elevated BPDE-Alb and PRS were linked to increased lung cancer risk, with the HR (95%CI) of 1.54 (1.36, 1.74) per SD increment in ln-transformed BPDE-Alb and 1.27 (1.14, 1.41) per SD increment in PRS, but high plasma Zn level was linked to a lower lung cancer risk [HR (95%CI)=0.77 (0.66, 0.91) per SD increment in ln-transformed Zn]. There was evidence of effect modification by Zn on BaP-lung cancer association (P for multiplicative interaction = 0.008). As Zn concentrations increased from the lowest to the highest tertile, the lung cancer risk per SD increment in ln-transformed BPDE-Alb decreased from 2.07 (1.48, 2.89) to 1.33 (0.90, 1.95). Additionally, we observed a significant synergistic interaction of BPDE-Alb and PRS [RERI (95%CI) = 0.85 (0.03, 1.67)], with 42% of the incident lung cancer cases among individuals with high BPDE-Alb and high PRS attributable to their additive effect [AP (95%CI) = 0.42 (0.14, 0.69)]. This study provided the first prospective epidemiological evidence that Zn has protective effect against BaP-induced lung tumorigenesis, whereas high genetic risk can enhance the harmful effect of BaP. These findings may provide novel insight into the environment-environment and environment-gene interaction underlying lung cancer development, which may help to develop prevention and intervention strategies to manage BaP-induced lung cancer.

Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction.

Whole-exome sequencing (WES) has been widely used to study the role of protein-coding variants in genetic diseases. Non-coding regions, typically covered by sparse off-target data, are often discarded by conventional WES analyses. Here, we develop a genotype calling pipeline named WEScall to analyse both target and off-target data. We leverage linkage disequilibrium shared within study samples and from an external reference panel to improve genotyping accuracy. In an application to WES of 2527 Chinese and Malays, WEScall can reduce the genotype discordance rate from 0.26% (SE= 6.4 × 10-6) to 0.08% (SE = 3.6 × 10-6) across 1.1 million single nucleotide polymorphisms (SNPs) in the deeply sequenced target regions. Furthermore, we obtain genotypes at 0.70% (SE = 3.0 × 10-6) discordance rate across 5.2 million off-target SNPs, which had ~1.2× mean sequencing depth. Using this dataset, we perform genome-wide association studies of 10 metabolic traits. Despite of our small sample size, we identify 10 loci at genome-wide significance (P < 5 × 10-8), including eight well-established loci. The two novel loci, both associated with glycated haemoglobin levels, are GPATCH8-SLC4A1 (rs369762319, P = 2.56 × 10-12) and ROR2 (rs1201042, P = 3.24 × 10-8). Finally, using summary statistics from UK Biobank and Biobank Japan, we show that polygenic risk prediction can be significantly improved for six out of nine traits by incorporating off-target data (P < 0.01). These results demonstrate WEScall as a useful tool to facilitate WES studies with decent amounts of off-target data.

Genetic and observational associations of lung function with gastrointestinal tract diseases: pleiotropic and mendelian randomization analysis.

BACKGROUND: The two-way communications along the gut-lung axis influence the immune function in both gut and lung. However, the shared genetic characteristics of lung function with gastrointestinal tract (GIT) diseases remain to be investigated. METHODS: We first investigated the genetic correlations between three lung function traits and four GIT diseases. Second, we illustrated the genetic overlap by genome-wide pleiotropic analysis (PLACO) and further pinpointed the relevant tissue and cell types by partitioning heritability. Furthermore, we proposed pleiotropic genes as potential drug targets by drug database mining. Finally, we evaluated the causal relationships by epidemiologic observational study and Mendelian randomization (MR) analysis. RESULTS: We found lung function and GIT diseases were genetically correlated. We identified 258 pleiotropic loci, which were enriched in gut- and lung-specific regions marked by H3K4me1. Among these, 16 pleiotropic genes were targets of drugs, such as tofacitinib and baricitinib targeting TYK2 for the treatment of ulcer colitis and COVID-19, respectively. We identified a missense variant in TYK2, exhibiting a shared causal effect on FEV1/FVC and inflammatory bowel disease (rs12720356, PPLACO=1.38 × 10- 8). These findings suggested TYK2 as a promising drug target. Although the epidemiologic observational study suggested the protective role of lung function in the development of GIT diseases, no causalities were found by MR analysis. CONCLUSIONS: Our study suggested the shared genetic characteristics between lung function and GIT diseases. The pleiotropic variants could exert their effects by modulating gene expression marked by histone modifications. Finally, we highlighted the potential of pleiotropic analyses in drug repurposing.

Efficacy comparison between iliosacral screw fixation of the posterior pelvic ring fracture with the assistance of modified percutaneous three-dimensional printing guide template and conventional fluoroscopy. / æ”¹è‰¯ç»çš®ä¸‰ç»´æ‰“å°å¯¼æ¿ä¸Žä¼ ç»Ÿé€è§†è¾ åŠ©éª¶é«‚èžºé’‰å›ºå®šéª¨ç›†åŽçŽ¯éª¨æŠ˜çš„ç–—æ•ˆæ¯”è¾ƒ.

OBJECTIVES: The effect of three-dimensional (3D) printed bone-attached guide plate assisted cannulated screw fixation of pelvic fracture is reliable, but extensive soft tissue dissection is still required when installing the guide plate. This study aims to compare the efficacy of posterior pelvic ring fracture fixation with iliosacral screw insertion between the assistance of modified percutaneous patient specific 3D printed guide template and conventional fluoroscopy. METHODS: From May, 2019 and September 2021, 28 patients sustained posterior pelvic ring fractures were randomized into 2 groups: A guide template group, in which the iliosacral screw was inserted for fixation of the posterior pelvic ring fracture with the assistance of modified percutaneous patient specific 3D printed guide template, and a fluoroscopy group, in which the iliosacral screw was inserted under the guidance of conventional fluoroscopy. The operation time, fluoroscopic frequency, intraoperative blood loss, and incision length were recorded for each screw insertion. Fracture reduction was evaluated according to the Matta criteria. The screw position was evaluated according to the modified Gras classification, and the functional outcome was evaluated according to Majeed score. The parameters of both groups were compared, and statistical analysis was performed. RESULTS: All the 28 patients were followed up for 12-24 months. Of them, 15 iliosacral screws were inserted in 14 patients in the guide template group, and 14 iliosacral screws were inserted in 14 patients in the fluoroscopy group. The operation time, fluoroscopic frequency, screw deviation, incision length, and blood loss in the guide template group were 20-30(25.8±2.8) min, 9-15(12.2±1.9), 2-4(2.6±0.7) mm, 4-5(4.6±0.5) cm, and 5-10 (7.8±1.7) mL, respectively, whereas those in the fluoroscopy group were 30-60(48.1±7.5) min, 40-96(64.7±16.3), 3-6(4.2±0.9) mm, 0.8-1.2(1.0±0.1) cm, and 2-5(3.1±1.3) mL, respectively, and there were statistical significance (all P<0.001). Fracture reduction was evaluated according to the Matta criteria, and all the patients reached excellence and good (P=0.584) in the 2 groups. According to modified Gras classification, there were 12 Grade I screws, 3 Grade II screws, and 0 Grade III screws in the guide template group, and 10 Grade I screws, 3 Grade II screws, and 1 Grade III screw in the fluoroscopy group, with no statistical significance (P=0.334). The functional outcome was evaluated according to Majeed score at the last follow-up, without significant difference between the guide template group and the fluoroscopy group (P=0.908). CONCLUSIONS: Compared with the conventional fluoroscopy, it would cost less operation time, less fluoroscopic frequency and increase more accurate screw insertion to fixate the posterior pelvic ring fracture with the assistance of modified percutaneous patient specific 3D printed guide template.

Monolithic integrated waveguide device with dual functions of electro-optic modulation and optical amplification.

An organic polymer-based monolithic integrated waveguide device with dual functions of electro-optic (EO) modulation and optical amplification is demonstrated. In this Letter, the dual functions are achieved by employing EO polymer as the waveguide upper cladding and organic optical amplified material as the waveguide core layer. Based on this dual-functional waveguide structure, the waveguide amplifier and the EO switch are successfully designed and fabricated on a SiO2-Si substrate. An optical gain of 5.8 dB at the wavelength of 1535 nm is obtained in the dual-functional polymer waveguide, and the EO switch based on the dual-functional polymer waveguide also presents a high-speed response time of ∼10ns.

Tetrakis(4-aminophenyl) ethene-doped perylene microcrystals with strong electrochemiluminescence for biosensing applications.

Perylene and its derivatives, as classical organic polycyclic aromatic hydrocarbon (PAH) ECL materials, have attracted extensive attention due to their excellent photoelectric activity and good structural controllability. As is well-known, the molecular structure of perylene is composed of five coplanar aromatic rings. There are intense π-π stacking interactions between perylene molecules, which lead to their aggregation and poor solubility in aqueous media. Unfortunately, this aggregation can weaken or even quench the emission intensity of perylene owing to the aggregation-caused quenching (ACQ) effect, finally limiting the analytical application of perylene in biological detection. In this work, perylene composite microcrystals (ETTA@Pe MCs) doped with non-planar molecular tetrakis(4-aminophenyl)ethene were synthesized in the aqueous phase by a surfactant-assisted self-assembly method. During this process, the intense π-π stacking interactions between perylene monomers were suppressed by doping. As a result, the ETTA@Pe MCs exhibited a significantly enhanced ECL signal as compared to that of perylene microcrystals (Pe MCs) in the presence of S2O82- as a co-reactant. Moreover, the ETTA@Pe MCs were utilized as a novel electrochemiluminescent (ECL) luminophores to fabricate a sensitive ECL biosensor for the quantitative analysis of dopamine (DA), which displayed a favorable linear response from 1 to 100 µmol L-1 with a detection limit of 0.96 nmol L-1.

Prolactin regulates LAT1 expression via STAT5 (signal transducer and activator of transcription 5) signaling in mammary epithelial cells of dairy cows.

The l-type amino acid transporter 1 (LAT1; also known as SLC7A5) is a transporter that allows the uptake of large neutral amino acids into mammalian cells. In dairy cows, LAT1 is highly expressed in lactating mammary tissues and involved in milk protein synthesis. Prolactin (PRL) has a lactogenic role and is capable of inducing milk production in ruminants. However, the relationship between PRL stimulation and LAT1 expression in dairy cow mammary gland has not been well understood. In this study, we showed that PRL stimulation increased expression of LAT1 and ß-casein in mammary epithelial cells of dairy cows. The stimulatory effect of PRL on milk protein production was inhibited by LAT1-specific inhibitor or LAT1 knockdown, suggesting that PRL-induced milk protein production is involved in LAT1 expression. To determine whether the PRL signaling pathway participates in regulation of LAT1 expression, PRLR (PRL receptor) or STAT5 (signal transducer and activator of transcription 5) was knocked down by short interfering (si)RNA in mammary epithelial cells of dairy cows. Western blot results showed that knockdown of PRLR or STAT5 with siRNA markedly decreased PRL-stimulated LAT1 expression. In addition, we observed a marked increase in plasma membrane expression of LAT1 in PRL-stimulated cells compared with control cells. These observations indicated that PRL signaling can regulate LAT1 expression and activity in mammary epithelial cells of dairy cows, contributing to increased amino acid availability and milk protein synthesis in mammary gland of dairy cow.

Examination of methionine stimulation of gene expression in dairy cow mammary epithelial cells using RNA-sequencing.

In this research communication, a cell model with elevated ß-CASEIN synthesis was established by stimulating bovine mammary epithelial cells with 0.6 mM methionine, and the genome-wide gene expression profiles of methionine-stimulated cells and untreated cells were investigated by RNA sequencing. A total of 458 differentially expressed genes (DEGs; 219 upregulated and 239 downregulated) were identified between the two groups. Gene Ontology (GO) analysis showed that the two highest-ranked GO terms in 'molecular function' category were 'binding' and 'catalytic activity', suggesting that milk protein synthesis in methionine-stimulated cells requires induction of gene expression to increase metabolic activity. Kyoto Encyclopedia of Genes and Genomes analysis revealed that within the 'environmental information processing' category, the subcategory that is most highly enriched for DEGs was 'signal transduction'. cGMP-PKG, Rap1, calcium, cAMP, PI3K-AKT, MAPK, and JAK-STAT are the pathways with the highest number of DEGs, suggesting that these signaling pathways have potential roles in mediating methionine-induced milk protein synthesis in bovine mammary epithelial cells. This study provides valuable insights into the physiological and metabolic adaptations in cells stimulated with methionine. Understanding the regulation of this transition is essential for effective intervention in the lactation process.

Electrochemiluminescence Enhanced by Restriction of Intramolecular Motions (RIM): Tetraphenylethylene Microcrystals as a Novel Emitter for Mucin 1 Detection.

Apart from the reported energy transfer mechanism of aggregation-induced electrochemiluminescence (AI-ECL) enhancement, a new strategy named restriction of intramolecular motions-driven ECL (RIM-ECL) enhancement is first proposed based on the phenomenon of a very strong electrochemiluminescence observed on the hexagonal tetraphenylethylene microcrystals (TPE MCs) in aqueous solution. Compared to TPE in molecule-isolation state with faint ECL, TPE in aggregate state (TPE MCs) showed a significantly enhanced ECL that was due to the restriction of intramolecular motions (RIM). Inspired by the unique luminescence characteristic of TPE MCs, we integrated the novel ECL emitter of TPE MCs and target-activated bipedal DNA walker together to fabricate a sensitive "off-on" ECL biosensor for Mucin 1 (MUC1) assay, which exhibited desirable linear response for a concentration scope from 1 fg/mL to 1 ng/mL with a low detection limit of 0.29 fg/mL. The RIM enhanced ECL demonstrated by the TPE MCs provides a new chapter in the exploration of aggregated organic emitters for further applications.

Ultra-sensitive polymeric waveguide temperature sensor based on asymmetric Mach-Zehnder interferometer.

We proposed and designed an ultra-sensitive polymeric waveguide temperature sensor based on an asymmetric Mach-Zehnder interferometer that has different widths in the two interferometer arms. A polymer with a larger thermo-optic coefficient (TOC) was employed to enhance the sensitivity of the waveguide temperature sensor. The influence of the width difference between the two arms and the cladding materials with different TOCs on the sensitivity of the sensor was studied and experimentally demonstrated. The devices were fabricated by using the standard photolithography and simple all-wet etching process. When the cladding material Norland optical adhesive 73 (NOA 73) and the width difference of 6.5 µm were selected, the sensitivity of the waveguide temperature sensor was measured to be 30.8 nm/°C. Moreover, the minimum temperature resolution was about 0.97×10-3°C. The proposed sensor has the distinct advantages of high sensitivity, high resolution, easy fabrication, low cost, and biological compatibility, which make it have potential applications in temperature detection of organisms, molecular analysis, and biotechnology.

Low power consumption thermo-optic switch formed by an integrated processing method.

In this paper, an integrated processing method was demonstrated to fabricate the polymer-based thermo-optic (TO) switch with low power consumption. The characteristic parameters of the switch were carefully designed and simulated. The air trench structure was exploited to reduce the power consumption, which can be formed with the waveguide simultaneously by the integrated processing method. Moreover, the introduced polymer/silica hybrid waveguide structure can also improve the response time of the device. A typical fabricated switch presented a low switching power of 5.2 mW. The measured switching rise time and fall time are 192.2 and 201.1 µs, respectively.

Functional analysis of the dairy cow mammary transcriptome between early lactation and mid-dry period.

In this research communication we used digital gene expression (DGE) analysis to identify differences in gene expression in the mammary glands of dairy cows between early lactation and the mid-dry period. A total of 741 genes were identified as being differentially expressed by DGE analysis. Compared with their expression in dry cows, 214 genes were up-regulated and 527 genes were down-regulated in lactating cow mammary glands. Gene Ontology analysis showed that lactation was supported by increased gene expression related to metabolic processes and nutrient transport and was associated with decreased gene expression related to cell proliferation. Pathway mapping using the Kyoto Encyclopedia of Genes and Genomes showed that 579 differentially expressed genes had pathway annotations related to 204 pathways. Metabolic pathway-related genes were the most significantly enriched. Genes and pathways identified by the present study provide insights into molecular events that occur in the mammary gland between early lactation and mid-dry period, which can be used to facilitate further investigation of the mechanisms underlying lactation and mammary tissue remodeling in dairy cows.

Fast and low-power thermo-optic switch based on organic-inorganic hybrid strip-loaded waveguides.

We design and fabricate a thermo-optic waveguide switch based on the configuration of a balanced Mach-Zehnder interferometer optimized for fast operation. The structure of the waveguides consists of two core layers with the lower layer formed with the high-index organic-inorganic hybrid material DR1/SiO2-TiO2. The hybrid material allows the mode field to be confined in an area for fast heat removal, and the formation of index tapers to expand the mode field at the two ends of the device to facilitate butt-coupling with single-mode fibers. Our typical fabricated device shows the same rise time and fall time of 80 µs and low switching power of 8.9 mW at the wavelength of 1550 nm.

Optimized design and fabrication of polymer/silica thermo-optic switch with low power consumption.

In this paper, the power-consumption characteristics of a polymeric thermo-optic (TO) switch consisting of a silica under-cladding on silicon substrate, a polymer core surrounded with polymer upper-cladding, and aluminum heating electrodes with different widths were investigated. Norland optical adhesive 73 with a larger TO coefficient was selected as the core layer, which could reduce the power consumption effectively. The silica under-cladding, with large thermal conductivity, could shorten the response time. The influences of the heating electrode width and the air trench structure on the power consumption of the device were systemically studied. A device with different widths of electrodes was fabricated by using conventional semiconductor fabrication techniques and measured with the planar optical waveguide testing system. Under 1550-nm wavelength, the power consumption of the device would be reduced from 23.27 to 4.35 mW, while the heating electrode width was decreased from 25 to 7 µm. Furthermore, it would be reduced to 1.7 mW after the air trench structure was employed. The switching time of the device was also measured, which was about 200 µs.

Three dimensional polymer waveguide using hybrid lithography.

A three dimensional polymer waveguide with taper structure was demonstrated and fabricated by a reliable and effective hybrid lithography. The hybrid lithography consists of lithography to fabricate a polymer waveguide and gray scale lithography to fabricate a polymer taper structure. Laser ablation and shadow aluminum evaporation were designed for gray scale lithography. The length of the gray scale region ranging from 20 to 400 µm could be controlled by the laser power, the ablation speed, and the aluminum thickness. The slope angle was determined by the length of the gray scale region and the thickness of the photoresist. The waveguide taper structure could be transferred to the lower layer by the etching method. The taper structure can be used for integration of the waveguide with different dimensions.

Dendritic arborization and spine dynamics are abnormal in the mouse model of MECP2 duplication syndrome.

MECP2 duplication syndrome is a childhood neurological disorder characterized by intellectual disability, autism, motor abnormalities, and epilepsy. The disorder is caused by duplications spanning the gene encoding methyl-CpG-binding protein-2 (MeCP2), a protein involved in the modulation of chromatin and gene expression. MeCP2 is thought to play a role in maintaining the structural integrity of neuronal circuits. Loss of MeCP2 function causes Rett syndrome and results in abnormal dendritic spine morphology and decreased pyramidal dendritic arbor complexity and spine density. The consequences of MeCP2 overexpression on dendritic pathophysiology remain unclear. We used in vivo two-photon microscopy to characterize layer 5 pyramidal neuron spine turnover and dendritic arborization as a function of age in transgenic mice expressing the human MECP2 gene at twice the normal levels of MeCP2 (Tg1; Collins et al., 2004). We found that spine density in terminal dendritic branches is initially higher in young Tg1 mice but falls below control levels after postnatal week 12, approximately correlating with the onset of behavioral symptoms. Spontaneous spine turnover rates remain high in older Tg1 animals compared with controls, reflecting the persistence of an immature state. Both spine gain and loss rates are higher, with a net bias in favor of spine elimination. Apical dendritic arbors in both simple- and complex-tufted layer 5 Tg1 pyramidal neurons have more branches of higher order, indicating that MeCP2 overexpression induces dendritic overgrowth. P70S6K was hyperphosphorylated in Tg1 somatosensory cortex, suggesting that elevated mTOR signaling may underlie the observed increase in spine turnover and dendritic growth.

Achieving high selectivity and activity of CO2 electroreduction to formate by in-situ synthesis of single atom Pb doped Cu catalysts.

Exploring highly selective and stable electrocatalysts is of great significance for the electrochemical conversion of CO2 into fuel. Herein, a three-dimensional (3D) nanostructure catalyst was developed by doping Pb single-atom (PbSA) in-situ on carbon paper (PbSA100-Cu/CP) through a low-energy and economical method. The designed catalyst exhibited abundant active sites and was beneficial to CO2 adsorption, activation, and subsequent conversion to fuel. Interestingly, PbSA100-Cu/CP showed a prominent Faraday efficiency (FE) of 97 % at -0.9 V versus reversible hydrogen electrode (vs. RHE) and a high partial current density of 27.9 mA·cm-2 for formate. Also, the catalyst remained significantly stable for 60 h during the durability test. The reaction mechanism was investigated by density functional theory (DFT), demonstrating that the doping PbSA induced the electrons redistribution, promoted the formate generation, reduced the rate-determining step (RDS) energy barrier, and inhibited the hydrogen evolution reaction. The study aims to provide a new strategy for developing of single-atom catalysts with high selectivity and stability, which will help reduce environmental pressure and alleviate energy problems.

Single-cell and Bulk Transcriptomic Analyses Reveal a Stemness and Circadian Rhythm Disturbance-related Signature Predicting Clinical Outcome and Immunotherapy Response in Hepatocellular Carcinoma.

AIMS: Investigating the impact of stemness-related circadian rhythm disruption (SCRD) on hepatocellular carcinoma (HCC) prognosis and its potential as a predictor for immunotherapy response. BACKGROUND: Circadian disruption has been linked to tumor progression through its effect on the stemness of cancer cells. OBJECTIVE: Develop a novel signature for SCRD to accurately predict clinical outcomes and immune therapy response in patients with HCC. METHODS: The stemness degree of patients with HCC was assessed based on the stemness index (mRNAsi). The co-expression circadian genes significantly correlated with mRNAsi were identified and defined as stemness- and circadian-related genes (SCRGs). The SCRD scores of samples and cells were calculated based on the SCRGs. Differentially expressed genes with a prognostic value between distinct SCRD groups were identified in bulk and single-cell datasets to develop an SCRD signature. RESULTS: A higher SCRD score indicates a worse patient survival rate. Analysis of the tumor microenvironment revealed a significant correlation between SCRD and infiltrating immune cells. Heterogeneous expression patterns, functional states, genomic variants, and cell-cell interactions between two SCRD populations were revealed by transcriptomic, genomic, and interaction analyses. The robust SCRD signature for predicting immunotherapy response and prognosis in patients with HCC was developed and validated in multiple independent cohorts. CONCLUSIONS: In summary, distinct tumor immune microenvironment patterns were confirmed under SCRD in bulk and single-cell transcriptomic, and SCRD signature associated with clinical outcomes and immunotherapy response was developed and validated in HCC.